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- PDB-6tiu: DROSOPHILA GTP-TUBULIN Y222F MUTANT -

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Basic information

Entry
Database: PDB / ID: 6tiu
TitleDROSOPHILA GTP-TUBULIN Y222F MUTANT
Components
  • Stathmin-4
  • Tubulin alpha-1 chain
  • Tubulin beta-1 chain
KeywordsCELL CYCLE / MICROTUBULE / MICROTUBULE DYNAMICS / MICROTULE NUCLEATION
Function / homology
Function and homology information


HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / astral microtubule / Neutrophil degranulation / lysosome localization / microtubule depolymerization / regulation of microtubule polymerization or depolymerization ...HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / astral microtubule / Neutrophil degranulation / lysosome localization / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / neuron projection development / mitotic cell cycle / growth cone / microtubule / hydrolase activity / neuron projection / GTPase activity / centrosome / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site ...Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin alpha-1 chain / Stathmin-4 / Tubulin beta-1 chain
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.571 Å
AuthorsGigant, B.
CitationJournal: J.Cell Biol. / Year: 2021
Title: GTP-dependent formation of straight tubulin oligomers leads to microtubule nucleation.
Authors: Ayukawa, R. / Iwata, S. / Imai, H. / Kamimura, S. / Hayashi, M. / Ngo, K.X. / Minoura, I. / Uchimura, S. / Makino, T. / Shirouzu, M. / Shigematsu, H. / Sekimoto, K. / Gigant, B. / Muto, E.
History
DepositionNov 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha-1 chain
B: Tubulin beta-1 chain
C: Tubulin alpha-1 chain
D: Tubulin beta-1 chain
E: Stathmin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,29919
Polymers217,1865
Non-polymers3,11314
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21460 Å2
ΔGint-198 kcal/mol
Surface area63610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.97, 126.35, 249.79
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 5 molecules ACBDE

#1: Protein Tubulin alpha-1 chain


Mass: 49989.266 Da / Num. of mol.: 2 / Mutation: K40R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: alphaTub84B, tubA84B, CG1913 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P06603
#2: Protein Tubulin beta-1 chain / Beta-1-tubulin


Mass: 50178.137 Da / Num. of mol.: 2 / Mutation: Y222F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: betaTub56D, CG9277 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q24560
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16851.133 Da / Num. of mol.: 1 / Mutation: S4A, C14A, F20W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63043

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Non-polymers , 4 types, 14 molecules

#4: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG1500, LISO4, PIPES BUFFER, PH 6.80

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.57→48 Å / Num. obs: 25304 / % possible obs: 98.7 % / Redundancy: 11.7 % / CC1/2: 0.997 / Net I/σ(I): 4.15
Reflection shellResolution: 3.57→3.79 Å / Mean I/σ(I) obs: 0.92 / Num. unique obs: 3723 / CC1/2: 0.565

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (3-OCT-2019)refinement
XDSdata processing
BUSTERphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3RYC

3ryc


Resolution: 3.571→48 Å / Cor.coef. Fo:Fc: 0.872 / Cor.coef. Fo:Fc free: 0.862 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.655
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 1266 -RANDOM
Rwork0.2208 ---
obs0.222 25301 98.7 %-
Displacement parametersBiso mean: 110.93 Å2
Baniso -1Baniso -2Baniso -3
1--7.9699 Å20 Å20 Å2
2--1.0433 Å20 Å2
3---6.9265 Å2
Refine analyzeLuzzati coordinate error obs: 0.6 Å
Refinement stepCycle: LAST / Resolution: 3.571→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14483 0 185 0 14668
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00814975HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9820317HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5202SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2630HARMONIC5
X-RAY DIFFRACTIONt_it14789HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1946SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact11012SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.81
X-RAY DIFFRACTIONt_other_torsion19.14
LS refinement shellResolution: 3.571→3.611 Å
RfactorNum. reflection% reflection
Rfree0.4218 26 -
Rwork0.3678 --
obs--60.12 %
Refinement TLS params.

T11: 1.5199 Å2 / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9379-1.0616-0.37972.33970.27511.4518-0.0074-0.02230.1183-0.0223-0.1164-0.08680.1183-0.08680.12380.01290.0140.1933-0.05010.01029.043431.531374.4158
21.4664-1.295-0.09372.36290.28491.37520.1285-0.15280.1097-0.1528-0.09360.14130.10970.1413-0.0349-0.01070.01740.1577-0.00190.07340.241770.221990.6225
30.503-0.85870.31091.63970.27480.95810.04090.0180.08890.0180.03590.18730.08890.1873-0.0768-0.0053-0.04530.1104-0.06580.0993-14.9212108.672102.134
41.41-0.46720.22611.29930.29931.43630.11680.1585-0.22280.1585-0.09280.1365-0.22280.1365-0.0239-0.02660.00010.1875-0.04290.0986-35.5213142.59115.648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|438 E|4 - E|64 }
2X-RAY DIFFRACTION2{ B|1 - B|432 E|65 - E|89 }
3X-RAY DIFFRACTION3{ C|1 - C|439 E|90 - E|115 }
4X-RAY DIFFRACTION4{ D|1 - D|431 E|116 - E|143 }

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